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What distribution do you have? Also, was it a 64-bit or 32-bit installation? Some 64-bit distributions change the output of uname to 'i686' so that scripts designed for 32-bit X86 processors won't tank when it returns 'x86_64' as the architecture.

Stick around and see if anyone else knows about this, but I'm not sure it's possible to upgrade a 32-bit install to a 64-bit one. I could be wrong. Either way it's probably easier just to install the 64-bit OS fresh.